Project ID: plumID:25.024
Name: Sampling glycan-glycan interactions for B22 calculations
Archive: https://github.com/IsabellGrothaus/Data_repository/raw/main/Grothaus_et_al_2025_B22_PLUMED.zip
Category: bio
Keywords: B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange
PLUMED version: 2.8
Contributor: Isabell Louise Grothaus
Submitted on: 27 Aug 2025
Publication: unpublished
PLUMED input files
| File | Compatible with |
|---|---|
| A2G2S2_longbox.dat |   |
| glucose_longbox.dat | |
Last tested: 27 Aug 2025, 16:42:48
Project description and instructions
Example plumed.dat (glucose_longbox.dat) file to sample COM-distance between two glucose molecules from a standard MD with restraints in x and y direction. Example plumed.dat (A2G2S2_longbox.dat) file to sample COM-distances between two complex N-glycan molecules with restraints in x and y. The distance is additionally biased via a metadynamics potential across multiple replica (RECT), where the glycan molecules are defined as the solute (hot) region (REST2) for enhanced sampling of their conformational phase space. Perform REST-RECT simulations of glycans in solution or bound as substrate to their respective enzyme. GROMACS 2022 was used.
Click here to open manual pages for actions used in this project.
Submission history
[v1] 27 Aug 2025: original submission
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